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Publication table displays first six authors, my name in bold, underlining indicates (co-)first authorship

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Dr. Alexander Shakeel Bates

I am a neuroscientist and computational biologist specialising in neuroanatomy, neurophysiology and connectomics of the insect brain. My research focuses on understanding how neural circuits wire and fire to generate complex behaviours, including olfactory processing and animal navigation. I develop open-source tools for neuroanatomical analysis and collaborate internationally on connectomics projects. In the wetlab, I use virtual reality and calcium imaging experiments to interrogate neurobiological circuits in living, behaving flies. I am a UK citizen.

total cites h index i10 index peer reviews
4312 21 24 25

Professional Research

Postdoctoral Fellow in Neurobiology

Harvard Medical School

Boston, US

present - 01/10/2020

  • Investigating navigational circuitry using calcium imaging, neurophysiology and behavioural studies involving virtual reality with Drosophila melanogaster, in the laboratory of Prof. Rachel Wilson
  • Co-leading an international collaboration with Prof. Wei-Chung Allen Lee, flywire and a network of international research groups on the first whole fly central nervous system connectome, open-access

Fellowships

Harvard Nomination for The Warren Alpert Distinguished Scholar Award

N/A

TBD

Current - 01/10/2022

  • Decision not yet made

Sir Henry Wellcome Fellowship

Wellcome Trust & University of Oxford

UK

01/02/2026 - 01/06/2022

  • 300,000 GBP towards my current research
  • Collaboration between groups of Rachel Wilson, Wei Lee, Scott Waddell and Jan Drugowitsch
  • Also accepted as Life Science Research Foundation fellow

EMBO fellow

European Molecular Biology Organization

Europe

01/06/2022 - 01/04/2021

  • Also accepted as a International Human Frontier Science Program fellow

Herchel Smith PhD Scholarship

Herchel Smith Foundation

Cambridge, UK

30/09/2019 - 01/08/2015

Boehringer Ingelheim PhD Scholarship

Boehringer Ingelheim Foundation

European

01/08/2018 - 01/08/2016

Education

Neuroscience PhD

MRC LMB, University of Cambridge

Cambridge, UK

30/02/2021 - 01/09/2015

Neuroscience BSc

University College London

London, UK

01/07/2015 - 01/09/2012

High School

Woodbridge High School

London, UK

01/09/2012 - 01/09/2008

  • 6 A*s at A-level, comprising: Physics, Chemistry, Mathematics, English Literature, Philosophy and Russian, and in a history related EPQ (level 3) project
  • 13 A*s at GCSE: English Literature, English Language, Mathematics, Statistics, Core Science, Additional Science, History, Philosophy, Geography, French, Italian, Russian and Expressive Arts. Jack Petchey Achievement Award

Primary Research

title author journal year cites
Distributed control circuits across a brain-and-cord connectome AS Bates, JS Phelps, M Kim, HH Yang, A Matsliah, Z Ajabi, E Perlman, … bioRxiv, in review at Nature 2025 11
Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster N Eckstein, AS Bates, A Champion, M Du, Y Yin, P Schlegel, AKY Lu, … Cell 2024 205
Information flow, cell types and stereotypy in a full olfactory connectome P Schlegel, AS Bates, T Stürner, SR Jagannathan, N Drummond, J Hsu, … Elife 2021 157
Complete connectomic reconstruction of olfactory projection neurons in the fly brain AS Bates, P Schlegel, RJV Roberts, N Drummond, IFM Tamimi, … Curr. Biology 2020 207
The natverse, a versatile toolbox for combining and analysing neuroanatomical data AS Bates, JD Manton, SR Jagannathan, M Costa, P Schlegel, T Rohlfing, … Elife 2020 206
Analysis and optimization of equitable US cancer clinical trial center access by travel time H Lee, AS Bates, S Callier, M Chan, N Chambwe, A Marshall, MB Terry, … JAMA oncology 2024 14
Functional and anatomical specificity in a higher olfactory centre S Frechter, AS Bates, S Tootoonian, MJ Dolan, J Manton, AR Jamasb, … eLife 2019 115
Neural circuit mechanisms for steering control in walking Drosophila A Rayshubskiy, SL Holtz, AS Bates, QX Vanderbeck, LS Capdevila, … ELife 2025 101
Quantitative Attributions with Counterfactuals DY Adjavon, N Eckstein, AS Bates, GSXE Jefferis, J Funke bioRxiv 2024 0
Whole-brain annotation and multi-connectome cell typing of Drosophila P Schlegel, Y Yin, AS Bates, S Dorkenwald, K Eichler, P Brooks, DS Han, … Nature 2024 333
Discriminative attribution from paired images N Eckstein, H Bukhari, AS Bates, GSXE Jefferis, J Funke Euro. Conf. on Computer Vision 2022 8
BAcTrace, a tool for retrograde tracing of neuronal circuits in Drosophila S Cachero, M Gkantia, AS Bates, S Frechter, L Blackie, A McCarthy, … Nature methods 2020 45
Neurogenetic dissection of the Drosophila lateral horn reveals major outputs, diverse behavioural functions, and interactions with the mushroom body MJ Dolan, S Frechter, AS Bates, C Dan, P Huoviala, RJ Roberts, … Elife 2019 167
Communication from learned to innate olfactory processing centers is required for memory retrieval in Drosophila MJ Dolan, G Belliart-Guérin, AS Bates, S Frechter, A Lampin-Saint-Amaux, … Neuron 2018 117
Automated reconstruction of a serial-section EM Drosophila brain with flood-filling networks and local realignment PH Li, LF Lindsey, M Januszewski, Z Zheng, AS Bates, I Taisz, M Tyka, … bioRxiv 2019 105
Sexual dimorphism in the complete connectome of the Drosophila male central nervous system S Berg, IR Beckett, M Costa, P Schlegel, M Januszewski, EC Marin, … bioRxiv 2025 4
Comparative connectomics of Drosophila descending and ascending neurons T Stürner, P Brooks, L Serratosa Capdevila, BJ Morris, A Javier, S Fang, … Nature 2025 35
A Drosophila computational brain model reveals sensorimotor processing PK Shiu, GR Sterne, N Spiller, R Franconville, A Sandoval, J Zhou, … Nature 2024 76
Network statistics of the whole-brain connectome of Drosophila A Lin, R Yang, S Dorkenwald, A Matsliah, AR Sterling, P Schlegel, S Yu, … Nature 2024 110
Neuronal wiring diagram of an adult brain S Dorkenwald, A Matsliah, AR Sterling, P Schlegel, SC Yu, CE McKellar, … Nature 2024 479
The connectome of the adult Drosophila mushroom body provides insights into function F Li, JW Lindsey, EC Marin, N Otto, M Dreher, G Dempsey, I Stark, … Elife 2020 381
A connectome and analysis of the adult Drosophila central brain LK Scheffer, CS Xu, M Januszewski, Z Lu, S Takemura, KJ Hayworth, … eLife 2020 1113
Connectomics analysis reveals first-, second-, and third-order thermosensory and hygrosensory neurons in the adult Drosophila brain EC Marin, L Büld, M Theiss, T Sarkissian, RJV Roberts, R Turnbull, … Curr. Biology 2020 105
Input connectivity reveals additional heterogeneity of dopaminergic reinforcement in Drosophila N Otto, MW Pleijzier, IC Morgan, AJ Edmondson-Stait, KJ Heinz, I Stark, … Curr. Biology 2020 80
Neural circuit basis of aversive odour processing in Drosophila from sensory input to descending output P Huoviala, MJ Dolan, FM Love, P Myers, S Frechter, S Namiki, … bioRxiv 2018 48
Combinatorial encoding of odors in the mosquito antennal lobe P Singh, S Goyal, S Gupta, S Garg, A Tiwari, V Rajput, AS Bates, … Nature Comm. 2023 17

Peer Review

journal reviews
COSYNE (abstracts) 9
PLoS Comp. Bio. 3
eLife 3
Nature Comm. 1

Reviews

title author journal year cites
Systems neuroscience: Auditory processing at synaptic resolution AS Bates, G Jefferis Curr. Biology 2022 1
Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics AS Bates, J Janssens, GS Jefferis, S Aerts Curr. opinion in neurobiology 2019 72

Selected Talks

4th Asia-Pacific Drosophila Neuroscience Conference (APDNC4)

N/A

Shenzhen, China

2026

  • Invited speaker

CSHL Neurobiology of Drosophila

N/A

Cold Spring Harbor, NY

2025

  • Invited speaker

FlyWire Townhall

N/A

Princeton, NJ

2025

  • Invited speaker

HMS Neurobiology Department Talk

N/A

Boston, MA

2025

CSHL Neuronal Circuits

N/A

Cold Spring Harbor, NY

2024

  • Invited speaker

ECRO meeting

European Chemoreception Research Organization

Trieste, Italy

2019

  • Invited speaker

Boehringer Ingelheim Meeting

Boehringer Ingelheim Fonds

Hirschegg, Austria

2018

MPI Connectomics meeting

Max Planck Institute

Berlin, Germany

2017

ECRO meeting

European Chemoreception Research Organization

Cambridge, UK

2017

Boehringer Ingelheim Meeting

Boehringer Ingelheim Fonds

Hirschegg, Austria

2017

Brains and Roses

Schaeffer and Datta group organised

Montserrat, Catalonia

2016

Selected Posters

HHMI Investigators’ Meeting

HHMI HQ

Chevy Chase

2023

UK Neural Computation

University of Nottingham

Nottingham, UK

2019

Boehringer Ingelheim Fonds communication workshop

Boehringer Ingelheim Foundation

Mainz, Germany

2017

Maggot Meeting

Janelia Research Campus

Ashburn, US

2016

High-resolution circuit reconstruction meeting

Janelia Research Campus

Ashburn, US

2016

LMB GSA Symposium

MRC LMB, University of Cambridge

Cambridge, UK

2016

Leadership

COSYNE 2026 abstract reviewer

COSYNE

N/A

2026

Teaching at the San Juan Winter School for Connectomics

San Juan Winter School

San Juan, Puerto Rico

2025

President of BlueSci

University College London

London, UK

01/10/2019 - 01/01/2016

  • Lead BlueSci, the University of Cambridge’s science media society, through 15 issues of the magazine

Officially mentored summer student

MRC LMB, University of Cambridge

Cambridge, UK

2018

Officially mentored undergraduate student

Dept. Zoology, University of Cambridge

Cambridge, UK

01/05/2018 - 01/09/2017

  • Student won best thesis in year award and two authorships

Officially mentored summer student

MRC LMB, University of Cambridge

Cambridge, UK

2017

LMB graduate symposium lead organiser

MRC LMB, University of Cambridge

Cambridge, UK

2017

LMB graduate symposium organiser

MRC LMB, University of Cambridge

Cambridge, UK

2016

President of the UCLU Writer’s Society

University College London

London, UK

01/10/2015 - 01/10/2014

Science Editor, Pi Magazine

University College London

London, UK

01/10/2015 - 01/10/2014

UCL iGEM 2014 Advisor

University College London

London, UK

2014

  • Project planning, oversight, team slection and management
  • Gold medallist

Most of my work has first been published on bioRxiv



Much of my work comes with open source R code

Other

Visiting Scholar

Janelia Research Campus

Ashburn, US

2019

Paris Spring School in Neuroscience Techniques

Paris Descartes University

Paris, France

2018

  • A course in Optical Imaging and Electrophysiological Recording in Neuroscience

Visiting Scholar

Janelia Research Campus

Ashburn, US

2016

University of Queensland Winter Scholarship

University of Queensland

Brisbane, Australia

2015

Amgen Scholarship

Dept. Zoology, University of Cambridge

Cambridge, UK

2014

UCL iGEM 2013 team member

University College London

London, UK

2013

  • Team member, cloning, cell culture, project planning
  • Gold medallist

Summer student in the biomolecular modelling laboratory

Cancer Research UK, London Research Institute

London, UK

2013

Data and Code

Public Dataset: BANC Adult Fly Brain Connectome

Harvard Dataverse

N/A

N/A

  • DOI: 10.7910/DVN/8TFGGB
  • Complete synaptic-resolution connectome of an adult female Drosophila melanogaster brain and ventral nerve cord

Open Source Contributions: natverse

GitHub Organization

N/A

N/A

Open Source Contributions: wilson-lab

GitHub Organization

N/A

N/A

Open Source Contributions: htem

GitHub Organization

N/A

N/A

Open Source Contributions: flyconnectome

GitHub Organization

N/A

N/A

Zenodo Dataset: Connectome Influence Calculator

Zenodo

N/A

N/A

Zenodo Dataset: Supplementary data to accompany Information flow, cell types and stereotypy in a full olfactory connectome

Zenodo

N/A

N/A

Zenodo Dataset: Supplemental Files for Eckstein and Bates et al., Cell (2024)

Zenodo

N/A

N/A

Zenodo Dataset: BAcTrace a new tool for retrograde tracing of neuronal circuits

Zenodo

N/A

N/A

Updated on 04/12/2025